oligo

DOI: 10.18129/B9.bioc.oligo    

This package is for version 3.11 of Bioconductor; for the stable, up-to-date release version, see oligo.

Preprocessing tools for oligonucleotide arrays

Bioconductor version: 3.11

A package to analyze oligonucleotide arrays (expression/SNP/tiling/exon) at probe-level. It currently supports Affymetrix (CEL files) and NimbleGen arrays (XYS files).

Author: Benilton Carvalho and Rafael Irizarry

Maintainer: Benilton Carvalho <benilton at unicamp.br>

Citation (from within R, enter citation("oligo")):

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("oligo")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("oligo")

 

PDF oligo User's Guide
PDF   Reference Manual
Text   NEWS

Details

biocViews DataImport, DifferentialExpression, ExonArray, GeneExpression, Microarray, OneChannel, Preprocessing, SNP, Software, TwoChannel
Version 1.52.1
In Bioconductor since BioC 2.0 (R-2.5) (13.5 years)
License LGPL (>= 2)
Depends R (>= 3.2.0), BiocGenerics(>= 0.13.11), oligoClasses(>= 1.29.6), Biobase(>= 2.27.3), Biostrings(>= 2.35.12)
Imports affyio(>= 1.35.0), affxparser(>= 1.39.4), DBI (>= 0.3.1), ff, graphics, methods, preprocessCore(>= 1.29.0), RSQLite (>= 1.0.0), splines, stats, stats4, utils, zlibbioc
LinkingTo preprocessCore
Suggests BSgenome.Hsapiens.UCSC.hg18, hapmap100kxba, pd.hg.u95av2, pd.mapping50k.xba240, pd.huex.1.0.st.v2, pd.hg18.60mer.expr, pd.hugene.1.0.st.v1, maqcExpression4plex, genefilter, limma, RColorBrewer, oligoData, BiocStyle, knitr, RUnit, biomaRt, AnnotationDbi, ACME, RCurl
SystemRequirements
Enhances doMC, doMPI
URL
Depends On Me ITALICS, maEndToEnd, oligoData, pd.081229.hg18.promoter.medip.hx1, pd.2006.07.18.hg18.refseq.promoter, pd.2006.07.18.mm8.refseq.promoter, pd.2006.10.31.rn34.refseq.promoter, pd.ag, pd.aragene.1.0.st, pd.aragene.1.1.st, pd.atdschip.tiling, pd.ath1.121501, pd.barley1, pd.bovgene.1.0.st, pd.bovgene.1.1.st, pd.bovine, pd.bsubtilis, pd.cangene.1.0.st, pd.cangene.1.1.st, pd.canine, pd.canine.2, pd.celegans, pd.charm.hg18.example, pd.chicken, pd.chigene.1.0.st, pd.chigene.1.1.st, pd.chogene.2.0.st, pd.chogene.2.1.st, pd.citrus, pd.clariom.d.human, pd.clariom.s.human, pd.clariom.s.human.ht, pd.clariom.s.mouse, pd.clariom.s.mouse.ht, pd.clariom.s.rat, pd.clariom.s.rat.ht, pd.cotton, pd.cyngene.1.0.st, pd.cyngene.1.1.st, pd.cyrgene.1.0.st, pd.cyrgene.1.1.st, pd.cytogenetics.array, pd.drogene.1.0.st, pd.drogene.1.1.st, pd.drosgenome1, pd.drosophila.2, pd.e.coli.2, pd.ecoli, pd.ecoli.asv2, pd.elegene.1.0.st, pd.elegene.1.1.st, pd.equgene.1.0.st, pd.equgene.1.1.st, pd.feinberg.hg18.me.hx1, pd.feinberg.mm8.me.hx1, pd.felgene.1.0.st, pd.felgene.1.1.st, pd.fingene.1.0.st, pd.fingene.1.1.st, pd.genomewidesnp.5, pd.genomewidesnp.6, pd.guigene.1.0.st, pd.guigene.1.1.st, pd.hc.g110, pd.hg.focus, pd.hg.u133.plus.2, pd.hg.u133a, pd.hg.u133a.2, pd.hg.u133a.tag, pd.hg.u133b, pd.hg.u219, pd.hg.u95a, pd.hg.u95av2, pd.hg.u95b, pd.hg.u95c, pd.hg.u95d, pd.hg.u95e, pd.hg18.60mer.expr, pd.ht.hg.u133.plus.pm, pd.ht.hg.u133a, pd.ht.mg.430a, pd.hta.2.0, pd.hu6800, pd.huex.1.0.st.v2, pd.hugene.1.0.st.v1, pd.hugene.1.1.st.v1, pd.hugene.2.0.st, pd.hugene.2.1.st, pd.maize, pd.mapping250k.nsp, pd.mapping250k.sty, pd.mapping50k.hind240, pd.mapping50k.xba240, pd.margene.1.0.st, pd.margene.1.1.st, pd.medgene.1.0.st, pd.medgene.1.1.st, pd.medicago, pd.mg.u74a, pd.mg.u74av2, pd.mg.u74b, pd.mg.u74bv2, pd.mg.u74c, pd.mg.u74cv2, pd.mirna.1.0, pd.mirna.2.0, pd.mirna.3.0, pd.mirna.3.1, pd.mirna.4.0, pd.moe430a, pd.moe430b, pd.moex.1.0.st.v1, pd.mogene.1.0.st.v1, pd.mogene.1.1.st.v1, pd.mogene.2.0.st, pd.mogene.2.1.st, pd.mouse430.2, pd.mouse430a.2, pd.mta.1.0, pd.mu11ksuba, pd.mu11ksubb, pd.nugo.hs1a520180, pd.nugo.mm1a520177, pd.ovigene.1.0.st, pd.ovigene.1.1.st, pd.pae.g1a, pd.plasmodium.anopheles, pd.poplar, pd.porcine, pd.porgene.1.0.st, pd.porgene.1.1.st, pd.rabgene.1.0.st, pd.rabgene.1.1.st, pd.rae230a, pd.rae230b, pd.raex.1.0.st.v1, pd.ragene.1.0.st.v1, pd.ragene.1.1.st.v1, pd.ragene.2.0.st, pd.ragene.2.1.st, pd.rat230.2, pd.rcngene.1.0.st, pd.rcngene.1.1.st, pd.rg.u34a, pd.rg.u34b, pd.rg.u34c, pd.rhegene.1.0.st, pd.rhegene.1.1.st, pd.rhesus, pd.rice, pd.rjpgene.1.0.st, pd.rjpgene.1.1.st, pd.rn.u34, pd.rta.1.0, pd.rusgene.1.0.st, pd.rusgene.1.1.st, pd.s.aureus, pd.soybean, pd.soygene.1.0.st, pd.soygene.1.1.st, pd.sugar.cane, pd.tomato, pd.u133.x3p, pd.vitis.vinifera, pd.wheat, pd.x.laevis.2, pd.x.tropicalis, pd.xenopus.laevis, pd.yeast.2, pd.yg.s98, pd.zebgene.1.0.st, pd.zebgene.1.1.st, pd.zebrafish, pdInfoBuilder, puma, pumadata, SCAN.UPC, waveTiling
Imports Me ArrayExpress, cn.farms, crossmeta, frma, ITALICS, mimager
Suggests Me BiocGenerics, fastseg, frmaTools, hapmap100khind, hapmap100kxba, hapmap500knsp, hapmap500ksty, hapmapsnp5, hapmapsnp6, maqcExpression4plex
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package oligo_1.52.1.tar.gz
Windows Binary oligo_1.52.1.zip (32- & 64-bit)
macOS 10.13 (High Sierra) oligo_1.52.1.tgz
Source Repository git clone https://git.bioconductor.org/packages/oligo
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/oligo
Package Short Url https://bioconductor.org/packages/oligo/
Package Downloads Report Download Stats

Documentation »

Bioconductor

R / CRAN packages and documentation

Support »

Please read the posting guide. Post questions about Bioconductor to one of the following locations: